Anti-Shigella flexneri variant Y antibody is a Mouse of Fab class that binds to an Shigella flexneri variant Y. The antibody binds an optimal trisaccharide epitope, a residue sequence BCD of the ABCD [f2)-R-L-Rha- (1f2)-R-L-Rha- (1f3)-R-L-Rha- (1f3)-â-D-GlcNAc- (1f] repeating unit of the O-polysaccharide of the S. flexneri variant Y LPS.
Figure 1 (Φ,Ψ) maps of the trajectories for the glycosidic linkages of 3RU segments of O-Ags Y and 2a.
Squares and stars indicate the bound conformations of ABCDA' pentasaccharide and deoxygenated BC*D to mAb SYA/J6, respectively. Circles and diamonds indicate the bound conformations of the nonreducing RU and middle RU of the synthetic [AB(E)CD]3 pentadecasaccharide to mAb F22-4, respectively.
Figure 2 Structure of the Fab fragment of the SYA/J6 antibody with bound octapeptide.
(A) Stereoview of the backbone trace with the octapeptide bound in the groove between the two variable domains (VL and VH). The CDRs of the light (L) chain and the heavy (H) chain are: L1 and H1 (green), L2 and H2 (gray), and L3 and H3 (yellow). VL and VH framework regions are in blue and mauve, respectively. The N terminus of the peptide is located at the ''lower end'' of the groove. The atom types for the peptide are: C, green; N, blue; O, red; and S, yellow. (B) Electrostatic surface potential (10 kT, red; neutral, white; 10 kT blue) of the same structure shown in A. Also shown are three water molecules (white spheres, in the order S2, S9, and S1 from top to bottom) lodged in the pocket in the deepest part of the groove (see also Fig. 2B). (C) Similar to B, but with bound pentasaccharide (sugar residues in the order Rha A, Rha B, Rha C, GlcNAc D, and Rha A from top to bottom) (data from ref. 11). The atom types for the sugar are: C, yellow; N, blue; and O, red. Rha C mainly occupies the groove pocket.
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